Manganese in PDB 5xsp: The Catalytic Domain of Gdpp with 5'-Papa
Protein crystallography data
The structure of The Catalytic Domain of Gdpp with 5'-Papa, PDB code: 5xsp
was solved by
F.Wang,
L.Gu,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
38.13 /
2.15
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
54.619,
117.263,
127.368,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
19.7 /
24.3
|
Manganese Binding Sites:
The binding sites of Manganese atom in the The Catalytic Domain of Gdpp with 5'-Papa
(pdb code 5xsp). This binding sites where shown within
5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the
The Catalytic Domain of Gdpp with 5'-Papa, PDB code: 5xsp:
Jump to Manganese binding site number:
1;
2;
3;
4;
Manganese binding site 1 out
of 4 in 5xsp
Go back to
Manganese Binding Sites List in 5xsp
Manganese binding site 1 out
of 4 in the The Catalytic Domain of Gdpp with 5'-Papa
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 1 of The Catalytic Domain of Gdpp with 5'-Papa within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn701
b:34.1
occ:1.00
|
OD2
|
A:ASP349
|
2.3
|
25.4
|
1.0
|
OD2
|
A:ASP497
|
2.3
|
28.3
|
1.0
|
OD1
|
A:ASP418
|
2.4
|
27.2
|
1.0
|
O
|
A:HOH821
|
2.4
|
29.2
|
1.0
|
NE2
|
A:HIS442
|
2.5
|
29.6
|
1.0
|
OD2
|
A:ASP418
|
3.0
|
29.1
|
1.0
|
CG
|
A:ASP418
|
3.0
|
27.4
|
1.0
|
O
|
A:HOH966
|
3.1
|
25.1
|
1.0
|
CG
|
A:ASP349
|
3.2
|
24.5
|
1.0
|
CG
|
A:ASP497
|
3.3
|
28.2
|
1.0
|
CD2
|
A:HIS442
|
3.5
|
30.5
|
1.0
|
CE1
|
A:HIS442
|
3.5
|
29.4
|
1.0
|
CB
|
A:ASP349
|
3.5
|
25.9
|
1.0
|
MN
|
A:MN702
|
3.5
|
62.7
|
1.0
|
OD1
|
A:ASP497
|
3.6
|
26.7
|
1.0
|
N
|
A:THR465
|
4.3
|
20.6
|
1.0
|
OG1
|
A:THR465
|
4.4
|
24.4
|
1.0
|
OD1
|
A:ASP349
|
4.4
|
22.5
|
1.0
|
CE1
|
A:HIS443
|
4.4
|
47.8
|
1.0
|
CB
|
A:ASP418
|
4.5
|
25.6
|
1.0
|
CA
|
A:SER464
|
4.5
|
25.7
|
1.0
|
NE2
|
A:HIS443
|
4.5
|
46.4
|
1.0
|
ND1
|
A:HIS442
|
4.6
|
31.1
|
1.0
|
CG
|
A:HIS442
|
4.6
|
31.1
|
1.0
|
CB
|
A:ASP497
|
4.6
|
28.0
|
1.0
|
CB
|
A:SER464
|
4.8
|
23.0
|
1.0
|
C
|
A:SER464
|
4.9
|
25.5
|
1.0
|
CA
|
A:ASP349
|
4.9
|
21.9
|
1.0
|
|
Manganese binding site 2 out
of 4 in 5xsp
Go back to
Manganese Binding Sites List in 5xsp
Manganese binding site 2 out
of 4 in the The Catalytic Domain of Gdpp with 5'-Papa
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 2 of The Catalytic Domain of Gdpp with 5'-Papa within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn702
b:62.7
occ:1.00
|
OD2
|
A:ASP418
|
2.4
|
29.1
|
1.0
|
O
|
A:HOH821
|
2.4
|
29.2
|
1.0
|
OD2
|
A:ASP347
|
2.5
|
34.0
|
1.0
|
NE2
|
A:HIS343
|
2.6
|
34.8
|
1.0
|
OD1
|
A:ASP347
|
2.9
|
32.1
|
1.0
|
CG
|
A:ASP347
|
3.1
|
30.6
|
1.0
|
CD2
|
A:HIS343
|
3.4
|
37.0
|
1.0
|
CG
|
A:ASP418
|
3.5
|
27.4
|
1.0
|
MN
|
A:MN701
|
3.5
|
34.1
|
1.0
|
CE1
|
A:HIS343
|
3.5
|
31.5
|
1.0
|
O
|
A:HOH966
|
3.9
|
25.1
|
1.0
|
OD1
|
A:ASP418
|
4.0
|
27.2
|
1.0
|
O
|
A:ASP418
|
4.5
|
25.7
|
1.0
|
CB
|
A:ASP347
|
4.5
|
24.2
|
1.0
|
CG
|
A:HIS343
|
4.5
|
32.3
|
1.0
|
ND1
|
A:HIS343
|
4.6
|
33.9
|
1.0
|
CB
|
A:ASP418
|
4.6
|
25.6
|
1.0
|
CB
|
A:ASP349
|
4.7
|
25.9
|
1.0
|
N
|
A:ALA350
|
4.7
|
22.0
|
1.0
|
CB
|
A:ALA350
|
4.8
|
23.4
|
1.0
|
OD1
|
A:ASP497
|
4.9
|
26.7
|
1.0
|
O
|
A:HOH904
|
4.9
|
30.0
|
1.0
|
OD2
|
A:ASP349
|
5.0
|
25.4
|
1.0
|
|
Manganese binding site 3 out
of 4 in 5xsp
Go back to
Manganese Binding Sites List in 5xsp
Manganese binding site 3 out
of 4 in the The Catalytic Domain of Gdpp with 5'-Papa
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 3 of The Catalytic Domain of Gdpp with 5'-Papa within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mn701
b:33.6
occ:1.00
|
O
|
B:HOH845
|
1.9
|
30.6
|
1.0
|
OD2
|
B:ASP349
|
2.3
|
24.5
|
1.0
|
OD2
|
B:ASP497
|
2.4
|
30.0
|
1.0
|
OD1
|
B:ASP418
|
2.4
|
26.5
|
1.0
|
NE2
|
B:HIS442
|
2.6
|
29.8
|
1.0
|
OD2
|
B:ASP418
|
2.8
|
23.9
|
1.0
|
CG
|
B:ASP418
|
2.9
|
25.8
|
1.0
|
CG
|
B:ASP349
|
3.3
|
26.5
|
1.0
|
O
|
B:HOH912
|
3.4
|
46.4
|
1.0
|
CG
|
B:ASP497
|
3.4
|
30.9
|
1.0
|
CD2
|
B:HIS442
|
3.4
|
25.8
|
1.0
|
MN
|
B:MN702
|
3.5
|
62.8
|
1.0
|
CE1
|
B:HIS442
|
3.6
|
31.1
|
1.0
|
CB
|
B:ASP349
|
3.6
|
23.2
|
1.0
|
OD1
|
B:ASP497
|
3.8
|
29.9
|
1.0
|
CE1
|
B:HIS443
|
4.3
|
41.6
|
1.0
|
NE2
|
B:HIS443
|
4.3
|
51.4
|
1.0
|
N
|
B:THR465
|
4.3
|
25.8
|
1.0
|
OG1
|
B:THR465
|
4.4
|
23.9
|
1.0
|
CB
|
B:ASP418
|
4.4
|
21.5
|
1.0
|
OD1
|
B:ASP349
|
4.4
|
24.7
|
1.0
|
CA
|
B:SER464
|
4.4
|
24.7
|
1.0
|
CG
|
B:HIS442
|
4.6
|
30.9
|
1.0
|
ND1
|
B:HIS442
|
4.6
|
29.3
|
1.0
|
CB
|
B:SER464
|
4.7
|
26.8
|
1.0
|
CB
|
B:ASP497
|
4.7
|
25.7
|
1.0
|
C
|
B:SER464
|
4.9
|
27.7
|
1.0
|
|
Manganese binding site 4 out
of 4 in 5xsp
Go back to
Manganese Binding Sites List in 5xsp
Manganese binding site 4 out
of 4 in the The Catalytic Domain of Gdpp with 5'-Papa
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 4 of The Catalytic Domain of Gdpp with 5'-Papa within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mn702
b:62.8
occ:1.00
|
O
|
B:HOH845
|
2.2
|
30.6
|
1.0
|
OD2
|
B:ASP418
|
2.5
|
23.9
|
1.0
|
OD2
|
B:ASP347
|
2.5
|
38.2
|
1.0
|
NE2
|
B:HIS343
|
2.6
|
31.2
|
1.0
|
OD1
|
B:ASP347
|
3.0
|
32.5
|
1.0
|
CG
|
B:ASP347
|
3.1
|
28.0
|
1.0
|
CD2
|
B:HIS343
|
3.4
|
29.6
|
1.0
|
CE1
|
B:HIS343
|
3.5
|
35.8
|
1.0
|
MN
|
B:MN701
|
3.5
|
33.6
|
1.0
|
CG
|
B:ASP418
|
3.5
|
25.8
|
1.0
|
O
|
B:HOH912
|
3.9
|
46.4
|
1.0
|
OD1
|
B:ASP418
|
4.1
|
26.5
|
1.0
|
O
|
B:ASP418
|
4.5
|
25.3
|
1.0
|
CG
|
B:HIS343
|
4.5
|
35.2
|
1.0
|
ND1
|
B:HIS343
|
4.5
|
37.8
|
1.0
|
CB
|
B:ASP347
|
4.6
|
29.6
|
1.0
|
CB
|
B:ASP418
|
4.7
|
21.5
|
1.0
|
OD1
|
B:ASP497
|
4.8
|
29.9
|
1.0
|
CB
|
B:ALA350
|
4.8
|
26.1
|
1.0
|
N
|
B:ALA350
|
4.8
|
25.7
|
1.0
|
CB
|
B:ASP349
|
4.8
|
23.2
|
1.0
|
OD2
|
B:ASP497
|
4.9
|
30.0
|
1.0
|
OD2
|
B:ASP349
|
5.0
|
24.5
|
1.0
|
|
Reference:
F.Wang,
Q.He,
K.Su,
T.Wei,
S.Xu,
L.Gu.
Structural and Biochemical Characterization of the Catalytic Domains of Gdpp Reveals A Unified Hydrolysis Mechanism For the Dhh/DHHA1 Phosphodiesterase Biochem. J. V. 475 191 2018.
ISSN: ESSN 1470-8728
PubMed: 29203646
DOI: 10.1042/BCJ20170739
Page generated: Sun Oct 6 03:28:49 2024
|